- Chimera-users - RBVI Mailing Lists

Request for authorization to use Chimera software
by Stany Tsom 03 Oct '24

03 Oct '24

Dear UCSF Chimera software Coordinator, I am Tsomene Stany Lionel, I have a master's degree in Organic Chemistry obtained at the University of Yaoundé 1, a well known University around central Africa, my studies was focused in isolation, synthesis, characterizations, in vitro and in silico studies, I have worked under the direction of Dr. Messi Angelique Nicolas. Since 2020, during the pandemic there is an increase demand in computerized aided research of bioactive compounds. At the same time, it helps us focus on specific bioactive compounds showing better results. At Yaoundé 1 University, there is a large need in learning and usage of your software for in silico purposes, that is for molecular docking studies, with your permission we will like to organize a series workshops at the University to help masters students, Ph D students and also Professors for the better understanding of molecular docking and help then have better results for their research purposes. We will like at the end of each workshop deliver a certificate for this software learning. Software coordinator, we will really be glad if you accept directing, giving us permission for this use of your software for these workshop Organization and while not coordinating this future. At the end we will with your permission co sign the certificates we will deliver to the participants. References Dr. Messi Angelique Nicolas, Senior Lecturer at University of Yaoundé 1 messiangeliquenicolas(a)gmail.com Dr. Ngomo Orleane , Senior Lecturer at University of Yaoundé 1 orleansn(a)yahoo.fr All the details of my informations are in the attachment -CV/resume - Masters degree (masters 2 and 1 transcripts) -Bachelors degree While waiting for an answer from you UCSF Chimera Software coordinator, receive my distinct greetings. Sincerely Tsomene stany

4 7

Software copyright consulting
by 姜恩誉 27 Sep '24

27 Sep '24

Hello, is the application of your Chimera X software for paper publication a non-commercial use？ Looking forward to your reply。 Thank you 姜恩誉 2023111025(a)stu.njau.edu.cn

2 2

Gaff type for Mn2+ to run antechamber
by Medhanjali Dasgupta 25 Sep '24

25 Sep '24

Dear all, I am trying to generate the electrostatic surface for a protein that contains Mn in the 2+ state in its active site. I've tried to go about it in two ways but keep getting stuck. 1. If I use chimera or Pymol to use the PDB2PQR-APBS plug in, it cannot find GAFF type for Mn2+ so it cannot run anyechamber to allocate the atomic charge to Mn2+. Am i missing an update? Is there any way to get around this? Can I run antechamber myself to recognise my ion of interest, and then determine the charge, input it into the .pqr file and run APBS? 2. I have used the online server hosted at poissonboltzmann.org to run pdb2pqr and apps but run into the problem of not knowing what the atomic charge is for Mn2+. Any help would be appreciated. Thanks!!! Medhanjali

2 5

question about non-standard amino acids
by Jessie Jaynes 23 Sep '24

23 Sep '24

Hi Folks, I have a short peptide (O=ornithine) FEFOGGOFEF Is it possible to construct this peptide in Chimera? Thank you, Jesse

2 1

Generating a single electrostatic potential surface for a protein + ligand complex
by jadeshi88＠gmail.com 22 Sep '24

22 Sep '24

Hi, New user to ChimeraX here, would really appreciate some help! I'm trying to generate an electrostatic potential surface for a protein-ligand complex. Currently, I am using the surface/coulombic, and surface ligand/coulombic ligand commands to generate surfaces separately for the protein and ligand, and then exporting to an .obj file. However, by doing so I'm left with two separate surface meshes, and what I really want is a single surface that encapsulates both entities. Is it possible to do this? Thanks in advance!

2 1

MD on Chimera
by Manon Bulliard 20 Sep '24

20 Sep '24

Good afternoon, I was using chimera to do molecular dynamic simulation. I had to download Chimera on my new computer and now have the 1.18 version. It seems this feature is not anymore present under Tools>MD/Ensemble Analysis>molecular dynamic simulation. Do you know where I can find it to still be able to perform my modeling as previously? Thank you in advance, Manon Manon Bulliard, PhD EPFL | ISREC | Prof. Constam group SV2837 | Station 19 | CH-1015 Lausanne manon.bulliard(a)epfl.ch

3 3

Need help to resolve the architecture
by Farida Aziz 20 Sep '24

20 Sep '24

Dear Sir/Madam, I want to install chimera (chimera-1.18-linux_x86_64.bin) on my ubuntu 24.04 LTS (apple mini mac M2) I am facing so many errors in installtion as shown below •/chimera-1.18-linux_x86_64.bin bash: •/chimera-1.18-linux_x86_64.bin: cannot execute binary file: Exec format error sudo •/chimera-1.16-linux_x86_64.bin [sudo] password for codebind:•/chimera-1.16-linux_x86_64. bin: 1: Syntax error: word unexpected (expecting ")") I used this command ''Uname -m '' to find the archetecture which is ''aarch64'' the binary file is ''x86_64''. Please help me to fix this problem, I this regards. will be very geatful. Thanking in anticipation. Rgards Dr.Farida

2 1

Selecting chain via command line
by Ellen Shrock 19 Sep '24

19 Sep '24

Hello, I am trying to write a script that will iterate through lists of PDB IDs, the relevant antibody chain labels within those PDBs, and antigen chain labels, and annotate the contacts between the antibody and antigen using the command findclash. After opening each PDB file, I am struggling to find a way to select the antibody chains as "sel1" and the antigen chain(s) as "sel2" since the command "select" does not seem to recognize chain labels. Could you please help me find a way to accomplish my goal? Thank you, Ellen

3 8

Python script to add hydrogens to selected carbon atoms
by Mandelli, Davide 19 Sep '24

19 Sep '24

Dear developers, I am trying to automatize a task using the chimera python interface. In the graphical user interface, I can get the result I want by performing the following actions: 1) Select a carbon atom (ctrl+left button) 2) Tools --> Structure Editing --> Build Structure 3) In the "Build Structure" window, select "Modify Structure" 4) Change selected atom to...: "Element C", "Bonds 4", "Geometry Tetrahedral" (basically the default) 5) Apply 6) Save as pdb Is it possible to create a python script to do 1-6 (repeating 1-5 for several carbon atoms identified by residue id and name)? I could then very easily prepare a bash script to apply these changes to hundreds of pdb files. I tried asking chatGPT for a quick answer, but most probably it is using python classes and methods that actually do not exist. Looking at the online documentation was also unsuccesful, but maybe you could point me to the right place. Thanks a lot! Best, Davide Dr Davide Mandelli Institute of Neuroscience and Medicine INM-9 Forschungszentrum Jülich Email: d.mandelli(a)fz-juelich.de<mailto:m.alfonso-prieto@fz-juelich.de> --------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------- Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Stefan Müller Geschaeftsfuehrung: Prof. Dr. Astrid Lambrecht (Vorsitzende), Karsten Beneke (stellv. Vorsitzender), Dr. Ir. Pieter Jansens --------------------------------------------------------------------------------------------- ---------------------------------------------------------------------------------------------

2 2

Error when opening session file cross-platform
by Alexander Lee 18 Sep '24

18 Sep '24

Apologies, I had accidentally sent this email to the ChimeraX platform. Now reposting it to the Chimera mail platform. I created a python session file on ubuntu and tried to open it on windows. Ubuntu was using Chimera 1.18 build 42535 but windows was using 1.18 build 42531. I've tried updating chimera on windows, but it said I was on the latest version already. When I open it on ubuntu on another desktop or from where I created it, it works. My session file is ~ 1.5 GB including smoothed trajectory. What should I do? Here are the outputs after running debug on windows: Cannot execute 'gzip': no automatic decompression of .Z files initializing general preferences loading Tix initializing graphics create application loading Pmw creating main window creating menus creating toolbar creating viewer initializing OpenGL initializing preferences initializing dialogs initializing COM initializing extensions Return code: -1073741819 Press return or enter to to exit [cid:0c988132-7bb8-429c-a6c7-f91f6db3b590] [cid:55bba9bf-1168-4782-b772-4d2e36e05e97]

3 3